Pneumovagina is a condition of perineal malconformation manifested by vulva inclination when more than 20% of the vulva opening is above the ischium of the pelvis that impairs fertility and is a concern among horse breeders. This study investigates the prevalence of pneumovagina and the contributing factors among mares in Kelantan. This study also elucidates the clinical manifestation of the oestrus behaviour from the reproductive hormones variation and the bacteriological profiles of the affected mares. One hundred and sixteen mares were selected purposively in this case-control study using structured questionnaires consisting of two parts: part one quantifies the signalments including age, breed, body condition score, age at first pregnancy, and number of pregnancies. Part two qualifies the oestrus behaviour detected using a stallion of each farm as a teaser. The vulva inclination angle of each mare was physically measured to determine the Caslick’s Index. Twenty mares were selected to analyse the hormonal response. Blood samples were taken on every other day for thirty days, reflecting one oestrus cycle. The plasma oestrogen and progesterone concentration were detected using an enzyme-immunosorbent assay with horse-oestrogen and horse-progesterone conjugate. The bacteria samples from vestibule, vagina, fornix, and uterus of thirty-four selected mares with various types of pneumovagina then were isolated and identified by the routine microbiology laboratory procedures. The E.coli was then analysed for the phylogenic group using quadruplet Clermont’s PCR method. E.coli from faecal sample was taken for group matching. The prevalence of pneumovagina among mares in Kelantan is 58% (n=67) which consists of 25% type-1, 16.3% type-2, and 16.3% type-3. The larger breed with poor body condition score (r2=0.1, P-value<0.05), young primiparous and multiparous mares (r2=0.1, P-value<0.05), were mostly with type-2 and type-3 pneumovagina. These mares showed inconsistent oestrus intervals (r2=-0.3, Pvalue< 0.05), and strong stallion reception (r2=0.2, P-value<0.05) during standing heat. The type-3 mares showed a significant difference of plasma oestrogen concentration in the waves pattern and amplitudes (P-value <0.05) that explains the irregular oestrus behaviour. The inconsistent wave patterns of progesterone suggest a delay in luteinizing hormone surge to facilitate ovulation that elucidated the extended oestrus and intense stallion-receptiveness behaviour in type-2 and type-3 pneumovaginal mares. The bacteria isolated from the reproductive tract was 72% from Enterobacteriacea family, and 6% from intestinal normo-flora. The type-3 pneumovagina has the highest bacterial isolates (88 isolates), of which 36.3% was from the fornix, 18.2% from the uterus, 34.1% from the vagina, and 11.36% from the vestibule. Low number of bacterial isolates in the uterus compared to the fornix was associated with the tight cervix during diestrous phase protecting the uterus. The phylogenic group of E.coli shows both commensal (58%) and pathogens (42%), which was similar to those from the faecal sample (P-value<0.05). This study discloses that the prevalence of pneumovagina is high in Kelantan, with severe types being the highest among those larger breed and poor body condition, young primiparous, and multiparous. The plasma oestrogen and progesterone concentration variation explain the inconsistency of oestrus interval and strong stallion-receptive behaviour. Most bacteria isolated from the reproductive tract were intestinal origin that matched those from the faeces, which reflects self-faeces contamination.